WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3jxv.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 25847.826
Volume of the Unit Cell V= 207255.656
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.009
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.650

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Nomenclature related problems

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 137 TYR   ( 287-)  A
 205 TYR   ( 355-)  A
 207 TYR   ( 357-)  A

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  54 PHE   ( 201-)  A
 160 PHE   ( 310-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 236 ASP   ( 386-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 167 GLU   ( 317-)  A
 178 GLU   ( 328-)  A
 182 GLU   ( 332-)  A
 195 GLU   ( 345-)  A
 204 GLU   ( 354-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 124 ASP   ( 273-)  A      CA   CB    1.63    5.2
 147 THR   ( 297-)  A      CA   CB    1.61    4.0
 147 THR   ( 297-)  A      CB   CG2   1.37   -4.7
 151 THR   ( 301-)  A      CA   CB    1.61    4.1
 153 LYS   ( 303-)  A      CE   NZ    1.61    4.1
 157 GLY   ( 307-)  A      N    CA    1.55    6.4
 163 LYS   ( 313-)  A      CB   CG    1.37   -4.9
 170 PRO   ( 320-)  A      N    CA    1.39   -5.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.995686  0.000563 -0.002494|
 |  0.000563  0.997151  0.000440|
 | -0.002494  0.000440  1.001679|
Proposed new scale matrix

 |  0.014526 -0.000009  0.002183|
 | -0.000018  0.032017 -0.000014|
 |  0.000026 -0.000005  0.010436|
With corresponding cell

    A    =  68.868  B   =  31.233  C    =  96.938
    Alpha=  89.960  Beta=  98.688  Gamma=  89.935

The CRYST1 cell dimensions

    A    =  69.168  B   =  31.322  C    =  96.716
    Alpha=  90.000  Beta=  98.460  Gamma=  90.000

Variance: 56.712
(Under-)estimated Z-score: 5.550

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  81 ALA   ( 228-)  A      N    CA   C    99.71   -4.1
 124 ASP   ( 273-)  A     -C    N    CA  133.46    6.5
 124 ASP   ( 273-)  A      C    CA   CB  100.98   -4.8
 147 THR   ( 297-)  A      C    CA   CB  119.30    4.8
 151 THR   ( 301-)  A      C    CA   CB  118.92    4.6
 151 THR   ( 301-)  A      CA   CB   OG1 116.02    4.3
 151 THR   ( 301-)  A      CG2  CB   OG1 119.14    4.9
 156 ASP   ( 306-)  A      N    CA   C    96.94   -5.1
 157 GLY   ( 307-)  A     -O   -C    N   112.70   -6.4
 157 GLY   ( 307-)  A     -CA  -C    N   126.41    5.1
 157 GLY   ( 307-)  A     -C    N    CA   99.74  -12.3
 223 THR   ( 373-)  A      N    CA   CB  121.29    6.3
 224 VAL   ( 374-)  A      N    CA   CB  102.97   -4.4
 224 VAL   ( 374-)  A      CA   CB   CG1 118.08    4.5
 224 VAL   ( 374-)  A      CA   CB   CG2 117.63    4.2
 224 VAL   ( 374-)  A      CG1  CB   CG2 124.03    6.0
 227 GLU   ( 377-)  A      CA   CB   CG  104.98   -4.6

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 167 GLU   ( 317-)  A
 178 GLU   ( 328-)  A
 182 GLU   ( 332-)  A
 195 GLU   ( 345-)  A
 204 GLU   ( 354-)  A
 236 ASP   ( 386-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 151 THR   ( 301-)  A      CB    -6.0    20.63    34.09
 158 THR   ( 308-)  A      CA    -7.4    21.41    33.84
 223 THR   ( 373-)  A      CA    -6.3    23.28    33.84
 224 VAL   ( 374-)  A      CB    22.6    -3.29   -32.96
The average deviation= 1.800

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 156 ASP   ( 306-)  A    4.85
  81 ALA   ( 228-)  A    4.15

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 124 ASP   ( 273-)  A    4.28

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 125 LYS   ( 274-)  A    -2.6
 178 GLU   ( 328-)  A    -2.4
  22 LYS   ( 169-)  A    -2.3
  51 GLY   ( 198-)  A    -2.1
 163 LYS   ( 313-)  A    -2.1
  52 VAL   ( 199-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   5 ASP   ( 152-)  A  omega poor
   8 LYS   ( 155-)  A  Poor phi/psi
   9 ASP   ( 156-)  A  Poor phi/psi, omega poor
  21 ASP   ( 168-)  A  omega poor
  22 LYS   ( 169-)  A  Poor phi/psi
  29 PRO   ( 176-)  A  omega poor
  34 VAL   ( 181-)  A  omega poor
  36 TYR   ( 183-)  A  omega poor
  61 LEU   ( 208-)  A  Poor phi/psi
  88 PHE   ( 235-)  A  omega poor
  96 ALA   ( 243-)  A  Poor phi/psi
 103 ASN   ( 252-)  A  Poor phi/psi
 114 SER   ( 263-)  A  Poor phi/psi
 124 ASP   ( 273-)  A  omega poor
 125 LYS   ( 274-)  A  Poor phi/psi
 136 GLY   ( 286-)  A  omega poor
 137 TYR   ( 287-)  A  Poor phi/psi
 138 GLU   ( 288-)  A  Poor phi/psi, omega poor
 150 ILE   ( 300-)  A  omega poor
 156 ASP   ( 306-)  A  Poor phi/psi
 157 GLY   ( 307-)  A  omega poor
 176 ASP   ( 326-)  A  Poor phi/psi
 178 GLU   ( 328-)  A  Poor phi/psi
 206 ALA   ( 356-)  A  Poor phi/psi
 214 GLN   ( 364-)  A  Poor phi/psi
 215 ASP   ( 365-)  A  omega poor
 221 ASN   ( 371-)  A  Poor phi/psi
 222 SER   ( 372-)  A  omega poor
 226 TYR   ( 376-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.741

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   4 ARG   ( 151-)  A      0
   6 ILE   ( 153-)  A      0
   7 ALA   ( 154-)  A      0
   8 LYS   ( 155-)  A      0
   9 ASP   ( 156-)  A      0
  21 ASP   ( 168-)  A      0
  22 LYS   ( 169-)  A      0
  23 TRP   ( 170-)  A      0
  25 ASN   ( 172-)  A      0
  29 PRO   ( 176-)  A      0
  48 LYS   ( 195-)  A      0
  50 GLU   ( 197-)  A      0
  58 ASP   ( 205-)  A      0
  60 HIS   ( 207-)  A      0
  61 LEU   ( 208-)  A      0
  62 CYS   ( 209-)  A      0
  71 THR   ( 218-)  A      0
  74 LYS   ( 221-)  A      0
  86 TYR   ( 233-)  A      0
  88 PHE   ( 235-)  A      0
  90 GLU   ( 237-)  A      0
  91 MET   ( 238-)  A      0
  93 ARG   ( 240-)  A      0
  95 ALA   ( 242-)  A      0
  96 ALA   ( 243-)  A      0
And so on for a total of 100 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.290

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 203 PRO   ( 353-)  A   1.60   10

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  29 PRO   ( 176-)  A    0.12 LOW
  84 PRO   ( 231-)  A    0.11 LOW
  94 PRO   ( 241-)  A    0.14 LOW
 170 PRO   ( 320-)  A    0.10 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 202 PRO   ( 352-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 203 PRO   ( 353-)  A  -124.8 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 124 ASP   ( 273-)  A      OD2 <->  205 TYR   ( 355-)  A      OH     0.79    1.61  INTRA BF
 151 THR   ( 301-)  A      CG2 <->  237 HOH   ( 410 )  A      O      0.44    2.36  INTRA BL
 156 ASP   ( 306-)  A      O   <->  157 GLY   ( 307-)  A      CA     0.34    2.06  INTRA BF
 138 GLU   ( 288-)  A      CG  <->  235 LYS   ( 385-)  A      NZ     0.34    2.76  INTRA BF
 174 LYS   ( 324-)  A      CD  <->  177 GLU   ( 327-)  A      OE2    0.32    2.48  INTRA BF
 137 TYR   ( 287-)  A      O   <->  138 GLU   ( 288-)  A      CB     0.31    2.29  INTRA BF
 124 ASP   ( 273-)  A      CG  <->  205 TYR   ( 355-)  A      OH     0.24    2.56  INTRA BF
 162 LYS   ( 312-)  A      CE  <->  167 GLU   ( 317-)  A      OE2    0.22    2.58  INTRA
 129 LYS   ( 278-)  A      CE  <->  195 GLU   ( 345-)  A      OE2    0.22    2.58  INTRA
 145 VAL   ( 295-)  A      CG1 <->  172 GLU   ( 322-)  A      CG     0.20    3.00  INTRA BF
 211 GLU   ( 361-)  A      OE2 <->  213 LYS   ( 363-)  A      NZ     0.18    2.52  INTRA BF
 146 VAL   ( 296-)  A      CG1 <->  148 VAL   ( 298-)  A      CG1    0.18    3.02  INTRA BL
   9 ASP   ( 156-)  A      OD2 <->   86 TYR   ( 233-)  A      OH     0.18    2.22  INTRA BF
  37 GLU   ( 184-)  A      OE2 <->   39 ARG   ( 186-)  A      NH1    0.17    2.53  INTRA BF
 177 GLU   ( 327-)  A      O   <->  178 GLU   ( 328-)  A      CB     0.16    2.44  INTRA BF
  39 ARG   ( 186-)  A      NH1 <->  109 ASP   ( 258-)  A      OD2    0.15    2.55  INTRA BF
 139 ARG   ( 289-)  A      NH1 <->  190 ASN   ( 340-)  A      O      0.14    2.56  INTRA BF
 156 ASP   ( 306-)  A      OD1 <->  158 THR   ( 308-)  A      CG2    0.14    2.66  INTRA
 153 LYS   ( 303-)  A      CE  <->  159 VAL   ( 309-)  A      CG2    0.13    3.07  INTRA BF
 156 ASP   ( 306-)  A      C   <->  157 GLY   ( 307-)  A      CA     0.13    2.17  INTRA BF
 177 GLU   ( 327-)  A      C   <->  178 GLU   ( 328-)  A      CB     0.12    2.68  INTRA BF
 162 LYS   ( 312-)  A      NZ  <->  167 GLU   ( 317-)  A      OE2    0.11    2.59  INTRA BL
  39 ARG   ( 186-)  A      O   <->  107 VAL   ( 256-)  A      N      0.10    2.60  INTRA BF
 121 ILE   ( 270-)  A      N   <->  127 ILE   ( 276-)  A      O      0.10    2.60  INTRA BL
 199 VAL   ( 349-)  A      N   <->  226 TYR   ( 376-)  A      O      0.10    2.60  INTRA BL
 153 LYS   ( 303-)  A      NZ  <->  157 GLY   ( 307-)  A      O      0.08    2.62  INTRA BF
 137 TYR   ( 287-)  A      C   <->  138 GLU   ( 288-)  A      CB     0.08    2.72  INTRA BF
   9 ASP   ( 156-)  A      C   <->   11 GLY   ( 158-)  A      N      0.08    2.82  INTRA BF
  93 ARG   ( 240-)  A      O   <->  100 VAL   ( 249-)  A      N      0.06    2.64  INTRA BL
  14 LYS   ( 161-)  A      NZ  <->   76 GLU   ( 223-)  A      OE2    0.04    2.66  INTRA BF
  69 VAL   ( 216-)  A      C   <->   71 THR   ( 218-)  A      N      0.04    2.86  INTRA BL
 136 GLY   ( 286-)  A      C   <->  137 TYR   ( 287-)  A      CG     0.04    3.06  INTRA BF
 139 ARG   ( 289-)  A      O   <->  235 LYS   ( 385-)  A      CD     0.04    2.76  INTRA BF
 207 TYR   ( 357-)  A      OH  <->  226 TYR   ( 376-)  A      OH     0.04    2.36  INTRA
 150 ILE   ( 300-)  A      O   <->  165 HIS   ( 315-)  A      CE1    0.04    2.76  INTRA BL
  39 ARG   ( 186-)  A      N   <->  107 VAL   ( 256-)  A      O      0.04    2.66  INTRA
 186 ARG   ( 336-)  A      O   <->  190 ASN   ( 340-)  A      ND2    0.03    2.67  INTRA BL
 212 SER   ( 362-)  A      OG  <->  214 GLN   ( 364-)  A      NE2    0.03    2.67  INTRA BF
 124 ASP   ( 273-)  A      OD2 <->  205 TYR   ( 355-)  A      CZ     0.03    2.77  INTRA BF
   9 ASP   ( 156-)  A      CB  <->   11 GLY   ( 158-)  A      N      0.03    3.07  INTRA BF
  83 LYS   ( 230-)  A      O   <->   86 TYR   ( 233-)  A      N      0.02    2.68  INTRA BF
  21 ASP   ( 168-)  A      N   <->   74 LYS   ( 221-)  A      O      0.02    2.68  INTRA BF
 121 ILE   ( 270-)  A      CG2 <->  122 GLY   ( 271-)  A      N      0.02    2.98  INTRA BL
 179 ALA   ( 329-)  A      C   <->  180 VAL   ( 330-)  A      CG1    0.01    3.09  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 137 TYR   ( 287-)  A      -8.84
  91 MET   ( 238-)  A      -6.34
 155 GLN   ( 305-)  A      -6.30
   8 LYS   ( 155-)  A      -5.69
  85 GLN   ( 232-)  A      -5.69
  50 GLU   ( 197-)  A      -5.27
 207 TYR   ( 357-)  A      -5.09
  90 GLU   ( 237-)  A      -5.06
  23 TRP   ( 170-)  A      -5.05

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  95 ALA   ( 242-)  A        97 - GLY    244- ( A)         -4.39
 167 GLU   ( 317-)  A       169 - GLU    319- ( A)         -4.31

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 237 HOH   ( 424 )  A      O     11.50   -1.11   46.16

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  25 ASN   ( 172-)  A
  60 HIS   ( 207-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   7 ALA   ( 154-)  A      N
  12 ILE   ( 159-)  A      N
  24 GLU   ( 171-)  A      N
  91 MET   ( 238-)  A      N
 126 LYS   ( 275-)  A      N
 137 TYR   ( 287-)  A      N
 141 ASN   ( 291-)  A      N
 156 ASP   ( 306-)  A      N
 176 ASP   ( 326-)  A      N
 180 VAL   ( 330-)  A      N
 216 ALA   ( 366-)  A      N
 223 THR   ( 373-)  A      N

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  30 ASP   ( 177-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.103
  2nd generation packing quality :   0.257
  Ramachandran plot appearance   :  -1.184
  chi-1/chi-2 rotamer normality  :  -1.741
  Backbone conformation          :   0.028

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.132
  Bond angles                    :   1.116
  Omega angle restraints         :   1.689 (loose)
  Side chain planarity           :   1.347
  Improper dihedral distribution :   1.735 (loose)
  B-factor distribution          :   0.603
  Inside/Outside distribution    :   1.019

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.08


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.132
  Bond angles                    :   1.116
  Omega angle restraints         :   1.689 (loose)
  Side chain planarity           :   1.347
  Improper dihedral distribution :   1.735 (loose)
  B-factor distribution          :   0.603
  Inside/Outside distribution    :   1.019
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.